Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate GFF3319 PGA1_c33720 D-cysteine desulfhydrase 2
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Phaeo:GFF3319 Length = 337 Score = 209 bits (532), Expect = 8e-59 Identities = 128/324 (39%), Positives = 181/324 (55%), Gaps = 17/324 (5%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68 LA+FPRV L TP++ + +S+E+G +++IKRDD TG+ GGNK RKLE+L+ +AL + Sbjct: 3 LARFPRVHLAHLSTPLEPMERLSKELGVELWIKRDDCTGMSTGGNKTRKLEFLMAEALEQ 62 Query: 69 GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKE-------ELKGNYLLDKIMGIE 121 GAD+V+T GA +NH T A KLGL ++L + GN LLD + G Sbjct: 63 GADMVMTQGATQTNHGRQTAAFAAKLGLKCHILLEDRTGYQDSNYNTNGNVLLDHLHGAT 122 Query: 122 TRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE-- 179 T + ++ E+ AE+++ +G K YVIP GG++P G LGYV A E+ +Q+ Sbjct: 123 TEKFPG--GHDMPGEMEKAAEKMRAKGHKVYVIPGGGSNPTGALGYVNAAFELVSQANDR 180 Query: 180 -VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELL 238 +K D +V A GS GT AGL G+ +N I +GI + +L + AE L Sbjct: 181 GLKIDRLVHATGSSGTQAGLVTGMCAMNAQIPVLGIGTRAPQPKQEQMIFDLACKTAEKL 240 Query: 239 G----VKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLA 294 G VK E DY YG T + I+ EGI+LDP Y+ K GL+DLA Sbjct: 241 GCAGIVKREDVMANTDYVGEGYGLPTQSGIEAIQMFAELEGILLDPCYSAKGGAGLIDLA 300 Query: 295 RKGEL-GEKILFIHTGGISGTFHY 317 RKGE GE+++F+HTGG + Y Sbjct: 301 RKGEFAGERVVFLHTGGAAALGGY 324 Lambda K H 0.319 0.142 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 298 Number of extensions: 17 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 325 Length of database: 337 Length adjustment: 28 Effective length of query: 297 Effective length of database: 309 Effective search space: 91773 Effective search space used: 91773 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory